Keto Pumpkin Cheesecake Cupcakes

This low-carb, high-fat ketogenic dessert has the right amount of sweetness and creaminess that you want without having to feel too guilty.
The original recipe calls for pumpkin pie spice in place of cinnamon; however, if it’s not available where you live try out this vanilla extract substitution with great results!

This keto pumpkin cheesecake cupcakes recipe is a delicious and easy dessert that is perfect for the holidays.

Keto Pumpkin Cheesecake Cupcakes

Cooking a diet-friendly pumpkin pie can be a real challenge. Traditionally high in carbs, both in the form of pumpkin puree and added sugars, this treat is hard to fit into standard keto macros. Don’t worry, we have a solution for you! If you’re on a keto diet but still want to meet your annual pumpkin pie ration, try these pumpkin cheesecake keto muffins!

The reason they fit so well into your keto diet is that we cut up a carbohydrate-rich pumpkin pie with a thick layer of cheesecake. A small amount of pumpkin in particular, is central to this recipe. These pumpkin cheese muffins are the perfect substitute for pumpkin pie this year. Moreover, they look great and will surely receive compliments from their loved ones!

How did you make them so beautiful?

It’s not one of those recipes where you see a picture and want to make it because it looks pretty, but once you make it, you end up with a mash that you have to eat right away. That way, no one will see the disaster you’ve created. These cheesecake muffins are easy to make and look as good as they do in the pictures. The trick is in the layering technique we use.

  1. First, form a crust on the bottom and bake to harden.
  2. Then add 2/3 of the cream cheese mixture to the top of the crust.
  3. Finally, stir in the remaining third of the cream cheese, stir in the mashed potatoes and add the pumpkin pie spice.
  4. Pour the pumpkin cheesecake mixture over the top and you’re done.

Can I use canned pumpkin pie mix?

Unfortunately, you can’t use canned cake mix for this low-carb pumpkin cheesecake recipe. Most canned pumpkin mixes contain a lot of sugar, which makes the carbohydrate count too high. We’ve thought of that and have a great low-carb option for you to make this dessert sweet and pumpkin-flavored without spiking blood sugar.

Advantages of canned pumpkin

100% canned pumpkin puree is not only delicious, it’s nutritious too! Although pumpkin puree has slightly more carbs, each keto pumpkin cheesecake has only 3.5 net carbs in the amount we use. Pumpkin also has many health benefits. Our keto pumpkin cheesecakes are rich in beta-carotene. This powerful antioxidant promotes healthy skin and good eyesight. In addition, our bodies can naturally convert beta-carotene into vitamin A, an essential vitamin, further enhancing these beneficial effects(1).

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Baking the perfect pumpkin cheesecake Keto

To make the best low-carb cheesecake, you need to follow a few important steps. With quality ingredients and a little love, we can make a hearty recipe for this holiday season. I’ve included information on ingredients, tips for getting a good crust and smooth bottom, and tips on how to make a perfect cheesecake every time. Follow these tips and tricks to make great keto recipes every time.

Coconut flour versus almond flour

Coconut flour is the main ingredient in our keto pumpkin cheesecake. It has a wonderful nutty flavor while increasing the fiber and volume of our crust. Unfortunately, coconut flour is very different from almond flour. Unlike coconut milk and almond milk, these two flours are not interchangeable. Almond flour is less able to absorb moisture, so more flour is needed to get a low-carb crust. Coconut flour is also nut-free and fairly inexpensive. Compared to almond flour, coconut flour is a great option for anyone who wants to make a low-carb dessert without breaking the bank.

All on this base

When making cheesecake, it’s important to create a solid base. I’ll explain below how to get the perfect silky texture, but first let’s talk about the ingredients. A common question about this recipe is why we add sour cream. The sour cream acts as an extra silky layer. Sometimes a regular cheesecake can be too cheesy. The sour cream adds a nice flavor that contrasts with the sweet vanilla base. This also makes for a looser cream that doesn’t get as compact and dense.

Another important ingredient is, of course, the sweetener! We used erythritol because its glycemic index is 1 and it has very few calories. There are several erythritol-based sweeteners you can try, but be aware that they can affect the final taste. We recommend that you stop using Swerve or Lakanto if you want to use another brand.

Baking the cake

The preparation of the crust is as important as the ingredients. When you make the cheesecake crust, make sure all the ingredients are well mixed and there are no lumps. To prevent the cream cheese filling from seeping into our keto cake, it’s important to bake it first. Preheat the oven to 350°F and bake the portioned and wrapped crusts for 12-15 minutes. Remove from oven and let cool before baking, and voila! You have a simple sugar-free keto cake.

How to get the perfect base for a keto cheesecake

All ingredients must be at room temperature! The best way to get a smooth mixture is to make sure all the ingredients are at room temperature. If you take one ingredient out of the fridge immediately and keep the rest warm, the cheesecake will become lumpy. This goes for cream cheese, whipped cream and even eggs!

Once you reach the last third of the dough, add the pumpkin puree and pumpkin spice and continue to stir for another minute to get all the lumps and spices into the dough.

Pumpkin pump!

I know that for me, like most people, pumpkin season is my thing! Because of all the fall foods and recipes, 90% of my diet consists of pumpkin. If this sounds like it for you too, try our many pumpkin-themed keto recipes!

  • Pumpkin Spice Latte – Is it really fall if you don’t make a simple PSL?
  • Low-carb pumpkin bread is a delicious spicy bread, perfect as a snack or even as a dessert. It also has its own soft cheesecake center, the perfect creamy flavor separating it from the overly sweet bread.
  • Pumpkin Pancakes – If you love breakfast, these pancakes will definitely be part of your routine. A super simple recipe that takes less than 20 minutes to make has never produced such a delicious brunch.

How to prevent cheesecake from breaking

This happens too often: The lovely fresh cheese mixture goes to the oven to bake. You leave and twenty minutes later there is already a huge crack in the cheesecake! It’s important to know what causes cracks so you can avoid them in this keto recipe.

  • Don’t bake cheesecake too long – Whether keto or not, baking cheesecake too long results in a dry surface that pulls and cracks. Make sure the center does not solidify completely. When it has cooled completely in the oven, bake it again. When you take the cheesecake out of the oven, it still needs a little stirring.
  • Cracks often occur when the cheesecake cools – if it sticks to the pan, it can pull to one side and cause a crack. We therefore recommend the use of non-stick silicones, which are generally better at preventing this phenomenon. Feel free to run a blunt knife across the silicone pan or baking sheet to prevent burning after baking.
  • Avoid the top of the oven – if you put the keto cheesecake in the top of the oven, it will start cooking on the top first. Try putting it in the middle on a medium grill to avoid overcooking the top.
  • Don’t beat the eggs too hard – if you beat the eggs too hard, too much air can get into the dough and create additional air bubbles that can fill and expand when heated. The temperature of the oven will be enough to crack them and make your perfect keto cheesecake.

Remember, even a cracked cheesecake is still delicious!

How to fix a cracked cheesecake

You’ve held everything, but your cheesecake is still blocked. It’s certainly boring, but not impossible. Unfortunately, there’s not much you can do about the cheesecake situation, but there are some great remedies you can use instead. Here are a few ideas for caulking stubborn cracks to keep your guests guessing!

  • The whipped cream was easy, as whipped cream goes well with all cheesecakes and gives them a delicate, light glaze. A nice contrast with the rich cheesecake.
  • Melted chocolate – Melt keto chocolate chips or try 100% melted chocolate mixed with stevia for a new topping. The chocolate covers all the cracks at the top and gives you a rich dessert. Know it will be chocolate and pumpkin, but it’s no less delicious!
  • Pumpkin glaze – need to make some at the last minute? Whip up our vanilla keto cream and spread it over the cheesecake. It’s low in carbs and you can even bring it more into the pumpkin theme by adding a tablespoon of pumpkin puree per serving.

What is pumpkin pie?

Pumpkin spice is a safe spice for the diet. It is a mixture of ground cinnamon, cloves, ginger and nutmeg. I recommend you find a recipe like this and make it yourself. You can also buy them quickly on amazon. If you don’t have time to wait for delivery and you feel comfortable going to the grocery store, check it out. Just make sure there is no added sugar.

Why does the cheesecake stick to the pan?

I usually use a skillet to make cheesecake. Pans with hinges are great for baking evenly, but often the crust sticks to the bottom and the cream cheese filling sticks to the inside. That’s why we didn’t use a springform pan, but a non-stick silicone muffin pan. An added benefit is that they bake much faster, and who doesn’t want a low-carb pumpkin cheesecake that fast! If you want to bake in a springform pan, I recommend this mini springform pan. Grease it well and add a few minutes to the cooking time to make sure it’s fully cooked.

Save some pumpkin cheesecake for later

Otherwise, you are depriving yourself of the chance to enjoy them in all their flavor. Did you know that you taste less when it’s hot! Trust me, you’ll want to put them in the fridge for 2-3 hours to cool. Once cooled to a comfortable temperature for cheesecake, they are ready. So go ahead, take it!

If you want to go crazy, you can drizzle these snacks with sugar-free whipped cream so your family thinks they’re eating a sweet treat.

Storage and freezing

They can be kept in the fridge for a good week. Just make sure they are in an airtight container and in the back of the fridge (which is coldest) if possible.

If you want to freeze a cheesecake, there is a special way to do it. Place the cheesecake on a clean cardboard circle. Wrap them tightly in plastic wrap and put them in a ziplock bag. Freeze for up to one month, after which the taste and consistency will be reduced. If you plan on eating them, take a few out of the freezer and refrigerate them ahead of time.

Fancy some more cheesecake? Try other easy keto recipes on our blog!

  • Strawberry Cheesecake – contains no sugar, but is packed with fresh fruit flavor.
  • Keto Cheesecake Pecan Bars – Looking for a recipe for a delicious pecan bar? These cheesecake bars are delicious! The sweet and salty combination with the vanilla cheesecake base is the perfect addition to your nightly treat.
  • White Chocolate Cheesecake – If you like sweeter desserts, this is the dessert for you. The sweet and very creamy white chocolate cheesecake is a new level of guilt-free decadence.
  • Low Carb Chocolate Cheesecake – Chocolate always makes a better dessert! Try our Chocolate Cheesecake recipe for a different take on the classic graham cracker crust.

Pumpkin Cheesecake Muffins

We’ll use it!

Total time 1 hour 30 minutes

For 11 cupcakes

Calorie content per serving 150,7 kcal

Cooking time: 20 minutes

Cooking time: 1 hour and 10 minutes


Pumpkin Cheesecake Filling



  • Mix the dry ingredients: Coconut flour, erythritol and salt. Set it aside.
  • In a separate bowl, mix the vanilla and melted coconut oil.
  • Slowly add the wet ingredients to the dry ingredients and mix thoroughly.
  • Add the hot lumps of butter and form a dough with your hands.
  • Pour the batter by hand into the bottom of each muffin tin in a greased muffin tin. We use a silicone cupcake pan.
  • Place the baking sheet in a preheated 350 degree oven for 12-15 minutes (depending on the thickness of the crust).
  • When cooked, remove and set aside to cool.


  • Beat room temperature cream cheese and erythritol with a hand mixer.
  • Add egg, sour cream and whipped cream. Keep stirring until everything is completely combined.
  • Use 2/3 of the batter, to fill the muffin tin.
  • Add pumpkin puree and pumpkin pie spice to remaining 1/3 of batter and mix well (remove lumps).
  • Slowly spread the remaining pumpkin cheesecake mixture (just made) over the cheesecake layer in the muffin tin.
  • Place in a preheated oven at 300 degrees for 55-60 minutes. Check with a toothpick to see if it goes through easily.
  • Place in the refrigerator and serve cold. Have fun!

Nutritional information

Pumpkin Cheesecake Muffins

Quantity per serving

Calories 150.7
Calories from fat 119

of the daily costs*.

Fat 13,2 g20 %.

Carbohydrates 5.4 g2%.

Fiber 1.9 g8%.

Protein 3g6%.

* Daily percentages are based on a 2000 calorie diet.



Keywords: Pumpkin Cheesecake Muffins

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Watch This Video-

These “enlightened keto pumpkin cheesecake” cupcakes are the perfect fall dessert. They’re low in carbs and sugar, but high on flavor!

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